log_parse.py
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# Copyright 2016 Vijayaditya Peddinti
# Vimal Manohar
# Apache 2.0.
from __future__ import division
from __future__ import print_function
import traceback
import datetime
import logging
import re
import libs.common as common_lib
logger = logging.getLogger(__name__)
logger.addHandler(logging.NullHandler())
g_lstmp_nonlin_regex_pattern = ''.join([".*progress.([0-9]+).log:component name=(.+) ",
"type=(.*)Component,.*",
"i_t_sigmoid.*",
"value-avg=\[.*=\((.+)\), mean=([0-9\.\-e]+), stddev=([0-9\.e\-]+)\].*",
"deriv-avg=\[.*=\((.+)\), mean=([0-9\.\-e]+), stddev=([0-9\.e\-]+)\].*",
"f_t_sigmoid.*",
"value-avg=\[.*=\((.+)\), mean=([0-9\.\-e]+), stddev=([0-9\.e\-]+)\].*",
"deriv-avg=\[.*=\((.+)\), mean=([0-9\.\-e]+), stddev=([0-9\.e\-]+)\].*",
"c_t_tanh.*",
"value-avg=\[.*=\((.+)\), mean=([0-9\.\-e]+), stddev=([0-9\.e\-]+)\].*",
"deriv-avg=\[.*=\((.+)\), mean=([0-9\.\-e]+), stddev=([0-9\.e\-]+)\].*",
"o_t_sigmoid.*",
"value-avg=\[.*=\((.+)\), mean=([0-9\.\-e]+), stddev=([0-9\.e\-]+)\].*",
"deriv-avg=\[.*=\((.+)\), mean=([0-9\.\-e]+), stddev=([0-9\.e\-]+)\].*",
"m_t_tanh.*",
"value-avg=\[.*=\((.+)\), mean=([0-9\.\-e]+), stddev=([0-9\.e\-]+)\].*",
"deriv-avg=\[.*=\((.+)\), mean=([0-9\.\-e]+), stddev=([0-9\.e\-]+)\]"])
g_normal_nonlin_regex_pattern = ''.join([".*progress.([0-9]+).log:component name=(.+) ",
"type=(.*)Component,.*",
"value-avg=\[.*=\((.+)\), mean=([0-9\.\-e]+), stddev=([0-9\.e\-]+)\].*",
"deriv-avg=\[.*=\((.+)\), mean=([0-9\.\-e]+), stddev=([0-9\.e\-]+)\]"])
g_normal_nonlin_regex_pattern_with_oderiv = ''.join([".*progress.([0-9]+).log:component name=(.+) ",
"type=(.*)Component,.*",
"value-avg=\[.*=\((.+)\), mean=([0-9\.\-e]+), stddev=([0-9\.e\-]+)\].*",
"deriv-avg=\[.*=\((.+)\), mean=([0-9\.\-e]+), stddev=([0-9\.e\-]+)\].*",
"oderiv-rms=\[.*=\((.+)\), mean=([0-9\.\-e]+), stddev=([0-9\.e\-]+)\]"])
class KaldiLogParseException(Exception):
""" An Exception class that throws an error when there is an issue in
parsing the log files. Extend this class if more granularity is needed.
"""
def __init__(self, message = None):
if message is not None and message.strip() == "":
message = None
Exception.__init__(self,
"There was an error while trying to parse the logs."
" Details : \n{0}\n".format(message))
# This function is used to fill stats_per_component_per_iter table with the
# results of regular expression.
def fill_nonlin_stats_table_with_regex_result(groups, gate_index, stats_table):
iteration = int(groups[0])
component_name = groups[1]
component_type = groups[2]
# for value-avg
value_percentiles = groups[3+gate_index*6]
value_mean = float(groups[4+gate_index*6])
value_stddev = float(groups[5+gate_index*6])
value_percentiles_split = re.split(',| ',value_percentiles)
assert len(value_percentiles_split) == 13
value_5th = float(value_percentiles_split[4])
value_50th = float(value_percentiles_split[6])
value_95th = float(value_percentiles_split[9])
# for deriv-avg
deriv_percentiles = groups[6+gate_index*6]
deriv_mean = float(groups[7+gate_index*6])
deriv_stddev = float(groups[8+gate_index*6])
deriv_percentiles_split = re.split(',| ',deriv_percentiles)
assert len(deriv_percentiles_split) == 13
deriv_5th = float(deriv_percentiles_split[4])
deriv_50th = float(deriv_percentiles_split[6])
deriv_95th = float(deriv_percentiles_split[9])
if len(groups) <= 9:
try:
if iteration in stats_table[component_name]['stats']:
stats_table[component_name]['stats'][iteration].extend(
[value_mean, value_stddev,
deriv_mean, deriv_stddev,
value_5th, value_50th, value_95th,
deriv_5th, deriv_50th, deriv_95th])
else:
stats_table[component_name]['stats'][iteration] = [
value_mean, value_stddev,
deriv_mean, deriv_stddev,
value_5th, value_50th, value_95th,
deriv_5th, deriv_50th, deriv_95th]
except KeyError:
stats_table[component_name] = {}
stats_table[component_name]['type'] = component_type
stats_table[component_name]['stats'] = {}
stats_table[component_name][
'stats'][iteration] = [value_mean, value_stddev,
deriv_mean, deriv_stddev,
value_5th, value_50th, value_95th,
deriv_5th, deriv_50th, deriv_95th]
else:
#for oderiv-rms
oderiv_percentiles = groups[9+gate_index*6]
oderiv_mean = float(groups[10+gate_index*6])
oderiv_stddev = float(groups[11+gate_index*6])
oderiv_percentiles_split = re.split(',| ',oderiv_percentiles)
assert len(oderiv_percentiles_split) == 13
oderiv_5th = float(oderiv_percentiles_split[4])
oderiv_50th = float(oderiv_percentiles_split[6])
oderiv_95th = float(oderiv_percentiles_split[9])
try:
if iteration in stats_table[component_name]['stats']:
stats_table[component_name]['stats'][iteration].extend(
[value_mean, value_stddev,
deriv_mean, deriv_stddev,
oderiv_mean, oderiv_stddev,
value_5th, value_50th, value_95th,
deriv_5th, deriv_50th, deriv_95th,
oderiv_5th, oderiv_50th, oderiv_95th])
else:
stats_table[component_name]['stats'][iteration] = [
value_mean, value_stddev,
deriv_mean, deriv_stddev,
oderiv_mean, oderiv_stddev,
value_5th, value_50th, value_95th,
deriv_5th, deriv_50th, deriv_95th,
oderiv_5th, oderiv_50th, oderiv_95th]
except KeyError:
stats_table[component_name] = {}
stats_table[component_name]['type'] = component_type
stats_table[component_name]['stats'] = {}
stats_table[component_name][
'stats'][iteration] = [value_mean, value_stddev,
deriv_mean, deriv_stddev,
oderiv_mean, oderiv_stddev,
value_5th, value_50th, value_95th,
deriv_5th, deriv_50th, deriv_95th,
oderiv_5th, oderiv_50th, oderiv_95th]
def parse_progress_logs_for_nonlinearity_stats(exp_dir):
""" Parse progress logs for mean and std stats for non-linearities.
e.g. for a line that is parsed from progress.*.log:
exp/nnet3/lstm_self_repair_ld5_sp/log/progress.9.log:component name=Lstm3_i
type=SigmoidComponent, dim=1280, self-repair-scale=1e-05, count=1.96e+05,
value-avg=[percentiles(0,1,2,5 10,20,50,80,90
95,98,99,100)=(0.05,0.09,0.11,0.15 0.19,0.27,0.50,0.72,0.83
0.88,0.92,0.94,0.99), mean=0.502, stddev=0.23],
deriv-avg=[percentiles(0,1,2,5 10,20,50,80,90
95,98,99,100)=(0.009,0.04,0.05,0.06 0.08,0.10,0.14,0.17,0.18
0.19,0.20,0.20,0.21), mean=0.134, stddev=0.0397]
"""
progress_log_files = "%s/log/progress.*.log" % (exp_dir)
stats_per_component_per_iter = {}
progress_log_lines = common_lib.get_command_stdout(
'grep -e "value-avg.*deriv-avg.*oderiv" {0}'.format(progress_log_files),
require_zero_status = False)
if progress_log_lines:
# cases with oderiv-rms
parse_regex = re.compile(g_normal_nonlin_regex_pattern_with_oderiv)
else:
# cases with only value-avg and deriv-avg
progress_log_lines = common_lib.get_command_stdout(
'grep -e "value-avg.*deriv-avg" {0}'.format(progress_log_files),
require_zero_status = False)
parse_regex = re.compile(g_normal_nonlin_regex_pattern)
for line in progress_log_lines.split("\n"):
mat_obj = parse_regex.search(line)
if mat_obj is None:
continue
# groups = ('9', 'Lstm3_i', 'Sigmoid', '0.05...0.99', '0.502', '0.23',
# '0.009...0.21', '0.134', '0.0397')
groups = mat_obj.groups()
component_type = groups[2]
if component_type == 'LstmNonlinearity':
parse_regex_lstmp = re.compile(g_lstmp_nonlin_regex_pattern)
mat_obj = parse_regex_lstmp.search(line)
groups = mat_obj.groups()
assert len(groups) == 33
for i in list(range(0,5)):
fill_nonlin_stats_table_with_regex_result(groups, i,
stats_per_component_per_iter)
else:
fill_nonlin_stats_table_with_regex_result(groups, 0,
stats_per_component_per_iter)
return stats_per_component_per_iter
def parse_difference_string(string):
dict = {}
for parts in string.split():
sub_parts = parts.split(":")
dict[sub_parts[0]] = float(sub_parts[1])
return dict
class MalformedClippedProportionLineException(Exception):
def __init__(self, line):
Exception.__init__(self,
"Malformed line encountered while trying to "
"extract clipped-proportions.\n{0}".format(line))
def parse_progress_logs_for_clipped_proportion(exp_dir):
""" Parse progress logs for clipped proportion stats.
e.g. for a line that is parsed from progress.*.log:
exp/chain/cwrnn_trial2_ld5_sp/log/progress.245.log:component
name=BLstm1_forward_c type=ClipGradientComponent, dim=512,
norm-based-clipping=true, clipping-threshold=30,
clipped-proportion=0.000565527,
self-repair-clipped-proportion-threshold=0.01, self-repair-target=0,
self-repair-scale=1
"""
progress_log_files = "%s/log/progress.*.log" % (exp_dir)
component_names = set([])
progress_log_lines = common_lib.get_command_stdout(
'grep -e "{0}" {1}'.format(
"clipped-proportion", progress_log_files),
require_zero_status=False)
parse_regex = re.compile(".*progress\.([0-9]+)\.log:component "
"name=(.*) type=.* "
"clipped-proportion=([0-9\.e\-]+)")
cp_per_component_per_iter = {}
max_iteration = 0
component_names = set([])
for line in progress_log_lines.split("\n"):
mat_obj = parse_regex.search(line)
if mat_obj is None:
if line.strip() == "":
continue
raise MalformedClippedProportionLineException(line)
groups = mat_obj.groups()
iteration = int(groups[0])
max_iteration = max(max_iteration, iteration)
name = groups[1]
clipped_proportion = float(groups[2])
if clipped_proportion > 1:
raise MalformedClippedProportionLineException(line)
if iteration not in cp_per_component_per_iter:
cp_per_component_per_iter[iteration] = {}
cp_per_component_per_iter[iteration][name] = clipped_proportion
component_names.add(name)
component_names = list(component_names)
component_names.sort()
# re arranging the data into an array
# and into an cp_per_iter_per_component
cp_per_iter_per_component = {}
for component_name in component_names:
cp_per_iter_per_component[component_name] = []
data = []
data.append(["iteration"]+component_names)
for iter in range(max_iteration+1):
if iter not in cp_per_component_per_iter:
continue
comp_dict = cp_per_component_per_iter[iter]
row = [iter]
for component in component_names:
try:
row.append(comp_dict[component])
cp_per_iter_per_component[component].append(
[iter, comp_dict[component]])
except KeyError:
# if clipped proportion is not available for a particular
# component it is set to None
# this usually happens during layer-wise discriminative
# training
row.append(None)
data.append(row)
return {'table': data,
'cp_per_component_per_iter': cp_per_component_per_iter,
'cp_per_iter_per_component': cp_per_iter_per_component}
def parse_progress_logs_for_param_diff(exp_dir, pattern):
""" Parse progress logs for per-component parameter differences.
e.g. for a line that is parsed from progress.*.log:
exp/chain/cwrnn_trial2_ld5_sp/log/progress.245.log:LOG
(nnet3-show-progress:main():nnet3-show-progress.cc:144) Relative parameter
differences per layer are [ Cwrnn1_T3_W_r:0.0171537
Cwrnn1_T3_W_x:1.33338e-07 Cwrnn1_T2_W_r:0.048075 Cwrnn1_T2_W_x:1.34088e-07
Cwrnn1_T1_W_r:0.0157277 Cwrnn1_T1_W_x:0.0212704 Final_affine:0.0321521
Cwrnn2_T3_W_r:0.0212082 Cwrnn2_T3_W_x:1.33691e-07 Cwrnn2_T2_W_r:0.0212978
Cwrnn2_T2_W_x:1.33401e-07 Cwrnn2_T1_W_r:0.014976 Cwrnn2_T1_W_x:0.0233588
Cwrnn3_T3_W_r:0.0237165 Cwrnn3_T3_W_x:1.33184e-07 Cwrnn3_T2_W_r:0.0239754
Cwrnn3_T2_W_x:1.3296e-07 Cwrnn3_T1_W_r:0.0194809 Cwrnn3_T1_W_x:0.0271934 ]
"""
if pattern not in set(["Relative parameter differences",
"Parameter differences"]):
raise Exception("Unknown value for pattern : {0}".format(pattern))
progress_log_files = "%s/log/progress.*.log" % (exp_dir)
progress_per_iter = {}
component_names = set([])
progress_log_lines = common_lib.get_command_stdout(
'grep -e "{0}" {1}'.format(pattern, progress_log_files))
parse_regex = re.compile(".*progress\.([0-9]+)\.log:"
"LOG.*{0}.*\[(.*)\]".format(pattern))
for line in progress_log_lines.split("\n"):
mat_obj = parse_regex.search(line)
if mat_obj is None:
continue
groups = mat_obj.groups()
iteration = groups[0]
differences = parse_difference_string(groups[1])
component_names = component_names.union(list(differences.keys()))
progress_per_iter[int(iteration)] = differences
component_names = list(component_names)
component_names.sort()
# rearranging the parameter differences available per iter
# into parameter differences per component
progress_per_component = {}
for cn in component_names:
progress_per_component[cn] = {}
max_iter = max(progress_per_iter.keys())
total_missing_iterations = 0
gave_user_warning = False
for iter in range(max_iter + 1):
try:
component_dict = progress_per_iter[iter]
except KeyError:
continue
for component_name in component_names:
try:
progress_per_component[component_name][iter] = component_dict[
component_name]
except KeyError:
total_missing_iterations += 1
# the component was not found this iteration, may be because of
# layerwise discriminative training
pass
if (total_missing_iterations/len(component_names) > 20
and not gave_user_warning and logger is not None):
logger.warning("There are more than {0} missing iterations per "
"component. Something might be wrong.".format(
total_missing_iterations/len(component_names)))
gave_user_warning = True
return {'progress_per_component': progress_per_component,
'component_names': component_names,
'max_iter': max_iter}
def get_train_times(exp_dir):
train_log_files = "%s/log/" % (exp_dir)
train_log_names = "train.*.log"
train_log_lines = common_lib.get_command_stdout(
'find {0} -name "{1}" | xargs grep -H -e Accounting'.format(train_log_files,train_log_names))
parse_regex = re.compile(".*train\.([0-9]+)\.([0-9]+)\.log:# "
"Accounting: time=([0-9]+) thread.*")
train_times = {}
for line in train_log_lines.split('\n'):
mat_obj = parse_regex.search(line)
if mat_obj is not None:
groups = mat_obj.groups()
try:
train_times[int(groups[0])][int(groups[1])] = float(groups[2])
except KeyError:
train_times[int(groups[0])] = {}
train_times[int(groups[0])][int(groups[1])] = float(groups[2])
iters = train_times.keys()
for iter in iters:
values = train_times[iter].values()
train_times[iter] = max(values)
return train_times
def parse_prob_logs(exp_dir, key='accuracy', output="output"):
train_prob_files = "%s/log/compute_prob_train.*.log" % (exp_dir)
valid_prob_files = "%s/log/compute_prob_valid.*.log" % (exp_dir)
train_prob_strings = common_lib.get_command_stdout(
'grep -e {0} {1}'.format(key, train_prob_files))
valid_prob_strings = common_lib.get_command_stdout(
'grep -e {0} {1}'.format(key, valid_prob_files))
# LOG
# (nnet3-chain-compute-prob:PrintTotalStats():nnet-chain-diagnostics.cc:149)
# Overall log-probability for 'output' is -0.399395 + -0.013437 = -0.412832
# per frame, over 20000 fra
# LOG
# (nnet3-chain-compute-prob:PrintTotalStats():nnet-chain-diagnostics.cc:144)
# Overall log-probability for 'output' is -0.307255 per frame, over 20000
# frames.
parse_regex = re.compile(
".*compute_prob_.*\.([0-9]+).log:LOG "
".nnet3.*compute-prob.*:PrintTotalStats..:"
"nnet.*diagnostics.cc:[0-9]+. Overall ([a-zA-Z\-]+) for "
"'{output}'.*is ([0-9.\-e]+) .*per frame".format(output=output))
train_objf = {}
valid_objf = {}
for line in train_prob_strings.split('\n'):
mat_obj = parse_regex.search(line)
if mat_obj is not None:
groups = mat_obj.groups()
if groups[1] == key:
train_objf[int(groups[0])] = groups[2]
if not train_objf:
raise KaldiLogParseException("Could not find any lines with {k} in "
" {l}".format(k=key, l=train_prob_files))
for line in valid_prob_strings.split('\n'):
mat_obj = parse_regex.search(line)
if mat_obj is not None:
groups = mat_obj.groups()
if groups[1] == key:
valid_objf[int(groups[0])] = groups[2]
if not valid_objf:
raise KaldiLogParseException("Could not find any lines with {k} in "
" {l}".format(k=key, l=valid_prob_files))
iters = list(set(valid_objf.keys()).intersection(list(train_objf.keys())))
if not iters:
raise KaldiLogParseException("Could not any common iterations with"
" key {k} in both {tl} and {vl}".format(
k=key, tl=train_prob_files, vl=valid_prob_files))
iters.sort()
return list([(int(x), float(train_objf[x]),
float(valid_objf[x])) for x in iters])
def parse_rnnlm_prob_logs(exp_dir, key='objf'):
train_prob_files = "%s/log/train.*.*.log" % (exp_dir)
valid_prob_files = "%s/log/compute_prob.*.log" % (exp_dir)
train_prob_strings = common_lib.get_command_stdout(
'grep -e {0} {1}'.format(key, train_prob_files))
valid_prob_strings = common_lib.get_command_stdout(
'grep -e {0} {1}'.format(key, valid_prob_files))
# LOG
# (rnnlm-train[5.3.36~8-2ec51]:PrintStatsOverall():rnnlm-core-training.cc:118)
# Overall objf is (-4.426 + -0.008287) = -4.435 over 4.503e+06 words (weighted)
# in 1117 minibatches; exact = (-4.426 + 0) = -4.426
# LOG
# (rnnlm-compute-prob[5.3.36~8-2ec51]:PrintStatsOverall():rnnlm-core-training.cc:118)
# Overall objf is (-4.677 + -0.002067) = -4.679 over 1.08e+05 words (weighted)
# in 27 minibatches; exact = (-4.677 + 0.002667) = -4.674
parse_regex_train = re.compile(
".*train\.([0-9]+).1.log:LOG "
".rnnlm-train.*:PrintStatsOverall..:"
"rnnlm.*training.cc:[0-9]+. Overall ([a-zA-Z\-]+) is "
".*exact = \(.+\) = ([0-9.\-\+e]+)")
parse_regex_valid = re.compile(
".*compute_prob\.([0-9]+).log:LOG "
".rnnlm.*compute-prob.*:PrintStatsOverall..:"
"rnnlm.*training.cc:[0-9]+. Overall ([a-zA-Z\-]+) is "
".*exact = \(.+\) = ([0-9.\-\+e]+)")
train_objf = {}
valid_objf = {}
for line in train_prob_strings.split('\n'):
mat_obj = parse_regex_train.search(line)
if mat_obj is not None:
groups = mat_obj.groups()
if groups[1] == key:
train_objf[int(groups[0])] = groups[2]
if not train_objf:
raise KaldiLogParseException("Could not find any lines with {k} in "
" {l}".format(k=key, l=train_prob_files))
for line in valid_prob_strings.split('\n'):
mat_obj = parse_regex_valid.search(line)
if mat_obj is not None:
groups = mat_obj.groups()
if groups[1] == key:
valid_objf[int(groups[0])] = groups[2]
if not valid_objf:
raise KaldiLogParseException("Could not find any lines with {k} in "
" {l}".format(k=key, l=valid_prob_files))
iters = list(set(valid_objf.keys()).intersection(list(train_objf.keys())))
if not iters:
raise KaldiLogParseException("Could not any common iterations with"
" key {k} in both {tl} and {vl}".format(
k=key, tl=train_prob_files, vl=valid_prob_files))
iters.sort()
return [(int(x), float(train_objf[x]),
float(valid_objf[x])) for x in iters]
def generate_acc_logprob_report(exp_dir, key="accuracy", output="output"):
try:
times = get_train_times(exp_dir)
except:
tb = traceback.format_exc()
logger.warning("Error getting info from logs, exception was: " + tb)
times = {}
report = []
report.append("%Iter\tduration\ttrain_objective\tvalid_objective\tdifference")
try:
if key == "rnnlm_objective":
data = list(parse_rnnlm_prob_logs(exp_dir, 'objf'))
else:
data = list(parse_prob_logs(exp_dir, key, output))
except:
tb = traceback.format_exc()
logger.warning("Error getting info from logs, exception was: " + tb)
data = []
for x in data:
try:
report.append("%d\t%s\t%g\t%g\t%g" % (x[0], str(times[x[0]]),
x[1], x[2], x[2]-x[1]))
except (KeyError, IndexError):
continue
total_time = 0
for iter in times.keys():
total_time += times[iter]
report.append("Total training time is {0}\n".format(
str(datetime.timedelta(seconds=total_time))))
return ["\n".join(report), times, data]